PXD055512-1

PXD055512 is an original dataset announced via ProteomeXchange.

Title	Comparison of MS Annika 3.0 against other crosslink search engines
Description	The field of crosslinking mass spectrometry has seen substantial advancements over the past decades, enabling the structural analysis of proteins and protein-complexes and serving as a powerful tool in protein-protein interaction studies. However, data analysis of large non-cleavable crosslink studies is still a mostly unsolved problem due to its n-squared complexity. We here introduce a novel algorithm for the identification of non-cleavable crosslinks implemented in our crosslinking search engine MS Annika that is based on sparse matrix multiplication and allows for proteome-wide searches on commodity hardware. Application of this new algorithm enabled us to employ a proteome-wide search of C. elegans nuclei samples and we were able to uncover previously unknown protein interactions and conclude a comprehensive structural analysis that provides a detailed view of the Box C/D complex, enhancing our understanding of its assembly and functional dynamics. Our findings provide valuable insights into the intricate regulation of cellular homeostasis and immune responses, which are conserved across species, including humans. Moreover, our algorithm will enable researchers to conduct similar studies that were previously unfeasible.
HostingRepository	PRIDE
AnnounceDate	2024-12-19
AnnouncementXML	Submission_2024-12-19_08:39:19.340.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Micha Johannes Birklbauer
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Streptoccous pyogenes; NCBI TaxID: 1314;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-03 04:33:21	ID requested
⏵ 1	2024-12-19 08:39:19	announced

10.1038/S42004-024-01386-X;

submitter keyword: non-cleavable, dss, adh, crosslinker,crosslinking

Viktoria Dorfer
contact affiliation	Bioinformatics Research Group, University of Applied Sciences Upper Austria, Softwarepark 11, Hagenberg, 4232, Upper Austria, Austria
contact email	viktoria.dorfer@fh-hagenberg.at
lab head
Micha Johannes Birklbauer
contact affiliation	University of Applied Sciences Upper Austria
contact email	micha.birklbauer@fh-hagenberg.at
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD055512
     1. Label: PRIDE project
     2. Name: Comparison of MS Annika 3.0 against other crosslink search engines